Contacts of the helix formed by residues 165 - 171 (chain C) in PDB entry 6QX2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C PHE* 1.4 83.1 - - + +
166C ASN* 1.3 58.1 + - - +
167C LEU 3.5 2.8 + - - -
168C LEU* 3.8 5.4 + - + -
169C ALA* 3.2 24.8 + - - +
188C LEU* 4.0 10.5 - - + -
191C LEU* 3.7 29.4 - - + +
192C ILE* 4.2 13.5 - - + -
195C VAL* 4.7 9.4 - - + -
352C LEU* 5.4 5.4 - - + -
355C TYR* 3.2 42.1 - - + +
473C LEU* 4.5 2.0 - - + -
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Residues in contact with ASN 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ARG 5.1 1.8 + - - -
40C ASP* 3.0 28.8 + - - +
41C GLY 4.1 5.5 + - - -
42C LEU* 3.5 21.2 - - - +
99C TYR* 5.6 0.8 - - - -
103C LEU* 4.0 6.7 - - - +
135C LEU* 3.9 23.0 - - + +
164C PHE* 3.0 25.1 + - + +
165C PRO* 1.3 70.5 - - - +
167C LEU* 1.3 65.5 + - - +
169C ALA* 4.0 0.9 - - - -
170C ASN* 2.8 55.2 + - - +
171C GLY 4.6 1.3 + - - +
355C TYR* 4.9 0.8 - - - -
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PRO* 3.7 31.6 - - + -
37C ASP 4.3 1.6 - - - +
38C VAL* 4.0 40.2 - - + +
39C ARG 5.5 0.8 + - - +
40C ASP 4.4 0.2 - - - -
41C GLY* 3.5 28.9 - - - +
165C PRO 3.5 0.8 - - - -
166C ASN* 1.3 76.7 - - - +
168C LEU* 1.3 62.2 + - + +
171C GLY* 2.9 32.3 + - - +
172C ALA* 4.4 4.0 - - + -
183C ILE* 3.9 24.3 - - + +
337C ALA* 4.2 9.2 - - + -
346C ILE* 4.5 7.6 - - + -
351C ALA* 4.8 8.5 - - + +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C PRO* 3.8 6.5 + - + +
167C LEU* 1.3 84.1 - - + +
169C ALA* 1.3 62.7 + - - +
170C ASN 3.4 0.2 - - - -
183C ILE* 4.1 16.6 - - + -
184C PRO 3.4 5.5 - - - +
185C PRO* 3.4 0.5 - - - +
186C HIS* 2.8 49.5 + - + +
191C LEU* 3.8 23.1 - - + -
234C TYR* 6.0 0.2 - - + -
335C MET* 4.3 14.4 - - - -
348C LEU* 3.9 21.8 - - + -
351C ALA* 4.1 22.4 - - + -
352C LEU* 3.8 29.6 - - + -
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG* 3.6 6.1 - - - +
101C TYR* 4.1 18.8 - - + -
164C PHE* 4.2 13.5 - - + -
165C PRO 3.2 22.0 + - - +
166C ASN* 3.3 8.9 + - - +
168C LEU* 1.3 76.3 - - - +
170C ASN* 1.3 59.4 + - - +
185C PRO* 3.3 6.6 - - - +
186C HIS 3.0 29.0 + - - +
188C LEU* 4.6 4.0 - - + -
191C LEU* 3.4 15.0 - - + +
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Residues in contact with ASN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C SER 4.8 7.8 - - - +
99C TYR* 3.3 29.1 - - + -
100C ARG 3.1 8.8 + - - -
101C TYR* 2.8 52.4 + - - +
103C LEU* 3.7 10.7 - - - +
164C PHE* 4.6 2.4 - - - -
166C ASN* 2.8 35.2 + - - +
169C ALA* 1.3 76.7 - - - +
171C GLY* 1.3 64.3 + - - +
185C PRO* 3.5 17.0 - - - +
266C PHE* 5.5 1.4 - - - -
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLY 4.7 5.9 - - - +
99C TYR* 5.6 3.6 + - - -
166C ASN* 4.6 1.6 + - - +
167C LEU 2.9 22.9 + - - +
168C LEU 3.7 0.8 + - - -
169C ALA 3.5 1.8 - - - -
170C ASN* 1.3 85.3 - - - +
172C ALA* 1.3 65.0 + - - +
183C ILE* 3.2 17.3 - - - -
184C PRO 3.9 11.2 - - - -
185C PRO* 4.8 0.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il